Textures and edges contribute different information to image recognition. Edges and boundaries encode shape information, while textures manifest the appearance of regions. Despite the success of Convolutional Neural Networks (CNNs) in computer vision and medical image analysis applications, predominantly only texture abstractions are learned, which often leads to imprecise boundary delineations. In medical imaging, expert manual segmentation often relies on organ boundaries; for example, to manually segment a liver, a medical practitioner usually identifies edges first and subsequently fills in the segmentation mask. Motivated by these observations, we propose a plug-and-play module, dubbed Edge-Gated CNNs (EG-CNNs), that can be used with existing encoder-decoder architectures to process both edge and texture information. The EG-CNN learns to emphasize the edges in the encoder, to predict crisp boundaries by an auxiliary edge supervision, and to fuse its output with the original CNN output. We evaluate the effectiveness of the EG-CNN with various mainstream CNNs on two publicly available datasets, BraTS 19 and KiTS 19 for brain tumor and kidney semantic segmentation. We demonstrate how the addition of EG-CNN consistently improves segmentation accuracy and generalization performance.
Multimodal brain tumor segmentation challenge (BraTS) brings together researchers to improve automated methods for 3D MRI brain tumor segmentation. Tumor segmentation is one of the fundamental vision tasks necessary for diagnosis and treatment planning of the disease. Previous years winning methods were all deep-learning based, thanks to the advent of modern GPUs, which allow fast optimization of deep convolutional neural network architectures. In this work, we explore best practices of 3D semantic segmentation, including conventional encoder-decoder architecture, as well combined loss functions, in attempt to further improve the segmentation accuracy. We evaluate the method on BraTS 2019 challenge.
Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. We validate their effectiveness on the task of brain tumor segmentation using the BraTS 2018 dataset. Our experiments reveal that our approach yields more accurate segmentation results, which makes it promising for more extensive application to medical image segmentation.
To validate a novel deformable image registration (DIR) method for online adaptation of planning organ-at-risk (OAR) delineations to match daily anatomy during hypo-fractionated RT of abdominal tumors.For 20 liver cancer patients, planning OAR delineations were adapted to daily anatomy using the DIR on corresponding repeat CTs. The DIR's accuracy was evaluated for the entire cohort by comparing adapted and expert-drawn OAR delineations using geometric (Dice Similarity Coefficient (DSC), Modified Hausdorff Distance (MHD) and Mean Surface Error (MSE)) and dosimetric (Dmax and Dmean) measures.For all OARs, DIR achieved average DSC, MHD and MSE of 86%, 2.1 mm, and 1.7 mm, respectively, within 20 s for each repeat CT. Compared to the baseline (translations), the average improvements ranged from 2% (in heart) to 24% (in spinal cord) in DSC, and 25% (in heart) to 44% (in right kidney) in MHD and MSE. Furthermore, differences in dose statistics (Dmax, Dmean and D2%) using delineations from an expert and the proposed DIR were found to be statistically insignificant (p > 0.01).The validated DIR showed potential for online-adaptive radiotherapy of abdominal tumors as it achieved considerably high geometric and dosimetric correspondences with the expert-drawn OAR delineations, albeit in a fraction of time required by experts.
Federated learning (FL) allows the collaborative training of AI models without needing to share raw data. This capability makes it especially interesting for healthcare applications where patient and data privacy is of utmost concern. However, recent works on the inversion of deep neural networks from model gradients raised concerns about the security of FL in preventing the leakage of training data. In this work, we show that these attacks presented in the literature are impractical in FL use-cases where the clients' training involves updating the Batch Normalization (BN) statistics and provide a new baseline attack that works for such scenarios. Furthermore, we present new ways to measure and visualize potential data leakage in FL. Our work is a step towards establishing reproducible methods of measuring data leakage in FL and could help determine the optimal tradeoffs between privacy-preserving techniques, such as differential privacy, and model accuracy based on quantifiable metrics. Code is available at https://nvidia.github.io/NVFlare/research/quantifying-data-leakage.
Textures and edges contribute different information to image recognition. Edges and boundaries encode shape information, while textures manifest the appearance of regions. Despite the success of Convolutional Neural Networks (CNNs) in computer vision and medical image analysis applications, predominantly only texture abstractions are learned, which often leads to imprecise boundary delineations. In medical imaging, expert manual segmentation often relies on organ boundaries; for example, to manually segment a liver, a medical practitioner usually identifies edges first and subsequently fills in the segmentation mask. Motivated by these observations, we propose a plug-and-play module, dubbed Edge-Gated CNNs (EG-CNNs), that can be used with existing encoder-decoder architectures to process both edge and texture information. The EG-CNN learns to emphasize the edges in the encoder, to predict crisp boundaries by an auxiliary edge supervision, and to fuse its output with the original CNN output. We evaluate the effectiveness of the EG-CNN with various mainstream CNNs on two publicly available datasets, BraTS 19 and KiTS 19 for brain tumor and kidney semantic segmentation. We demonstrate how the addition of EG-CNN consistently improves segmentation accuracy and generalization performance.
Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at: https://github.com/RagMeh11/QU-BraTS.
Segmentation is a critical step in analyzing the developing human fetal brain.There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation.However, FeTA 2021 was a single center study, and the generalizability of algorithms across different imaging centers remains unsolved, limiting real-world clinical applicability.The multi-center FeTA Challenge 2022 focuses on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI).In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two imaging centers as well as two additional unseen centers.The data from different centers varied in many aspects, including scanners used, imaging parameters, and fetal brain super-resolution algorithms applied.16 teams participated in the challenge, and 17 algorithms were evaluated.Here, a detailed overview and analysis of the challenge results are provided, focusing on the generalizability of the submissions.Both in-and out of domain, the white matter and ventricles were segmented with the highest accuracy, while the most challenging structure remains the cerebral cortex due to anatomical complexity.The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multiclass fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms.The resulting new methods contribute to improving the analysis of brain development in utero. 1
Lesion segmentation in medical imaging has been an important topic in clinical research. Researchers have proposed various detection and segmentation algorithms to address this task. Recently, deep learning-based approaches have significantly improved the performance over conventional methods. However, most state-of-the-art deep learning methods require the manual design of multiple network components and training strategies. In this paper, we propose a new automated machine learning algorithm, T-AutoML, which not only searches for the best neural architecture, but also finds the best combination of hyper-parameters and data augmentation strategies simultaneously. The proposed method utilizes the modern transformer model, which is introduced to adapt to the dynamic length of the search space embedding and can significantly improve the ability of the search. We validate T-AutoML on several large-scale public lesion segmentation data-sets and achieve state-of-the-art performance.
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